Navios Quick Reference

Navios Quick Reference Purpose: The purpose of this Quick Reference is to provide a simple step by step outline of the information needed to perform various tasks on the system. We begin with basic tasks like starting up or shutting down the system and then proceed to more involved software tasks. It is organized according to the modules in the Navios Flow Cytometer Training Modules. Major Headings (in blue) are the major groups of tasks. These headings may be further subdivided into subsections of the major task and appear in a logical sequence. For example, the Major task of creating a protocol is subdivided into the subsections: Select Parameters, Create Plots, Instrument Settings, Create Regions, Gate, Analyze, and Save Protocol. A list of the major tasks appears below in the Table of Contents. Table of Contents Startups P. 3 Shutdown P. 4 Creating a Protocol P. 5 Create a FlowPAGE P. 7 AutoSetup P. 8 Acquisition Manager (Panels) P. 9 Database P. 11 Offline Analysis P. 15 System Setup P. 19 1

Startups Check external Sheath tank, fill the Cleaning agent tank and Empty the Waste tank Power the Computer and Monitor On Select User and enter a Windows password if any and select OK Double click icon. Select User name Enter User password and select Next Select Connect (to run samples) or Work Offline. Check gages System Pressure 30 Psi, Vac 17 in (Cytometer only) Menus Resource Explorer Focus object Workspace Toolbars Worklist file tab Protocols file tab Listmode file tab Plot Acquisition Manager Panel file tab Current Workspace protocol Tabs Commonly Used Toolbars: File Toolbar Save LMD Print Copy Undo PRISM Histogram Rectangle Elliptical PRISM Multilinear Gates Color Publish File Plot Plot Divider 2 region Blend Help Open LMD Save Cut Paste Redo Dot Density Polygon Quadrant Contour Linear PRISM Color 2 Zoom Calculate Stats

File Protocol Plot Plot region Divider 1 Precedence Cytometer Toolbar Start Pause & Rotate Abort Shutdown Clenz Manual Mode Cytometer Control Restart Pause Stop Flow Rate Prime Single Tube Fixed Mode Open Worklist Save Panel Add Tube Customize Worklist Autoscheduler Acquisition Manager Toolbar New Worklist Save Worklist Delete Current Add Panel Print Open External Tasks Worklist Order Shutdown Place 2 ml of 10 % bleach solution in one tube Place 2 ml of de-ionized water in each of 3 tubes Select on the toolbar to clear the Acq. Mgr. Select the tab on the Resource Explorer Select the Common Folder Select the cleanse.pnl and drag and drop it to the Acq. Mgr. Enter a carousel number Select button Select Yes if you wish to save the previous protocol or No if not When the panel is finished, remove all tubes Select Standby mode When finished select in the upper right to exit the software Select No Select to turn off the cytometer Select Start >> Shutdown >> OK to shutdown the computer 3

Creating a Protocol Select File >> New >> New Protocol to clear the workspace of all but one dotplot and single elliptical gate region. Select Yes to save old protocol or No if you do not wish to save it Select Parameters: Select Cytometer Control on the toolbars Select Acquisition Setup tab Set Limits and Max events to stop accumulation later Select button Deselect unwanted parameters Select any desired parameters Optional: Set Ratio, Time and Derived Parameters Close shutters of unused lasers Select FS Collection angle and SS desired ND filter Select Yes, enter a name and select Save Create Plots: Dot Plots (2 parameter) Select, Histogram Plot (Single parameter) Select, Density plot Select Select Parameter(s) and then OK Repeat for each plot Select each plot Focus (top of the plot) in turn and drag the plot to the desired location on the Workspace Press CTRL + T, select plot size, and then OK to arrange plots Instrument Settings: Select Single Tube Mode on the toolbar Place a sample for the application in position 10 on the carousel Select Run Select Cytometer Control and then the Acq. Setup tab Select Setup Mode and QuickSET Choose discriminator parameter and adjust Discriminator to exclude debris and noise but pass cells Adjust the slider bars (top and side of each plot) beginning with those to be used as gates for a correct pattern Select Acq. Setup tab If needed, select QuickCOMP and adjust the compensation using a proper sample until correct patterns are seen 4

Deselect Setup Mode, QuickSET, and QuickCOMP Allow the system to collect the desired amount of data Select to stop or allow the system to reach a stop value Create Regions Select each plot in turn and add regions: Dot Plots (2 Parameter Plots only): Polygon - select Move the cursor to starting point on plot and left click Use a click move technique to create all the sides back to the starting point Rectangle select Move the cursor to the starting corner and left click Move the cursor to the opposite corner and left Click to complete the rectangle Quadrant Select Move the cursor to plot and left click Move the region to anchor position and left click Autgogate Select ellipse or contour Move the cursor to desired population and left click Histogram Plots: Linear Select Move the cursor to starting position and left click Move the cursor to ending position and left click Multilinear Select Move the cursor to first position and left click Move the cursor to end of first region and left click Move the cursor to end of second region and left click Continue until all regions have been created Move cursor to and left click to finish Gate Move the cursor to lower right corner of plot to be gated When appears, left click and select Gate If you wish to apply the gate to all plots select that option (Note: later ungate the plot containing the gate region) Optional: Stop Count Select Stop and Save tab and enter count Analyze Select Analysis >> Select Results Deselect all unwanted statistics and select all desired statistics and Select OK Save Protocol Select File >> Save Protocol or Select 5

Create a FlowPAGE Select Insert >> Blank Flow Page Move the new page to a convenient area of the screen Add Plots Move the cursor to the center of a plot Left click and drag and drop it onto the FlowPAGE Repeat for each plot Arrange Plots Select the Maximize Window icon in the upper right corner of the FlowPAGE to expand the page to full screen Move each plot and move into position OR Create a large rectangle completely encircling two plots and stats Select the appropriate alignment tool ( top, bottom, left or right) Add Text Select on the FlowPAGE toolbar Move the cursor to the location on the page and left click Type in desired text and select OK Reshape the text box by grabbing a handle and pulling outward Right click in the box and select Properties to change font, fill, etc. Left click on another part of the page to finish Add Images Select on the FlowPAGE toolbar Locate the directory where the image is stored Select the desired image and then Open Move the cursor to the desired location on the page and left click Use the handles to resize the image Left click on another part of the page to finish Add Lines or Boxes Select or Move to the starting point Hold the left button and drag to the ending point Save FlowPAGE Select FlowPAGE >> Save FlowPAGE As Enter a name and select Save 6

AutoSetup Note: To enter a new application, you will need a base protocol and target channels for Flow-Set Pro New Application Select Tools >> AutoSetup Application Definition Select Create a new application definition Select Current user only or All users as desired Select Next Browse to find the base protocol that represents the application Select the base protocol and then Open Select Next Select Filter Block and then Next Optional: select dyes Select Next Enter the correct Flow-Set Pro target channels Select Next Enter an application name and select Next Select Create a verification protocol if you wish the system to generate a verification protocol Or Select Add additional verifier, locate the protocol, and select Open to add a verification protocol Select Next The system summarizes your entries Select Print if you wish and then Finish The system now creates all protocols and FlowPAGES needed for Autostandardization Schedule an Select Tools >> AutoSetup Scheduler Application Select desired application Or Hold the CTRL key down and select multiple applications Enter a carousel number and select Schedule Select Run if you wish to run immediately Or Select Close to prep tubes, place them on the system, or enter a calibration factor in the Acquisition Manager Select on the toolbar to run the samples 7

Acquisition Manager (Panels) If it is not visible, select View (or right click) Select Acquisition Manager Select Columns Select View >> Customize Worklist Columns Select the desired columns to appear and then OK Edit Column Names Select View >> Customize Worklist Columns Left click on the column name until the name can be changed Type in the new name and press Enter When finished, select OK Create a Panel Select to clear the Acquisition Manager Select protocol tab on the Resource Explorer Drag and drop the desired first protocol to the Acquisition Manager Select the on the toolbar to add the desired number of tubes to the panel If you wish to change the protocol in any of the tubes, select the Open Protocol in the Protocol column for that tube Select the desired protocol and then Open Repeat as necessary for each tube Under Regions column, toggle the appropriate icon: to use the regions in that protocol, to carry the region to the other tubes, or to import regions from another protocol Under the Cytosettings column, toggle the appropriate icon to: to use the cytosettings in the protocol, to pass the cytosettings to the next protocol, or to import cytosettings from another protocol Select Open Edit the Parameter names for each tube to reflect the actual measurements (example: CD3, CD4, etc.) To Delete a Protocol Select the protocol line by its number and press Delete To Move a Protocol Select the protocol and drag and drop to the new position 8

Save Panel Right click on Panel folder or panel area in Acq. Mgr. Enter a panel name If you desire to create a template in the database for Reporting results, select Export results of panel to Report Generator on the Panel Save Dialog Select Save Create a Worklist Select Clear Worklist to clear the Acq. Mgr. then: To Add Panels Select Panels tab on the Resource Explorer Locate the desired panel and drag and drop it to the Acquisition Manager Repeat as desired To Add Protocols Select Protocols tab on the Resource Explorer Locate the desired protocol and drag and drop it to the Acquisition Manager Repeat as desired Editing Parameter Select the desired field (e.g. Under P1, P2, etc) Names Type in the desired information (e.g. Sample ID, Parameter name, etc.) Save Worklist Select Save Worklist on the toolbars Enter a worklist name and select Save To Run Select to clear Acquisition Manager Select Worklist tab on Resource Explorer Locate the desired worklist and drag and drop it to the Acquisition Manager Edit the boxes as desired To add Cal Factor, click on in the Cal Factor column of the Acquisition Manager Enter absolute count calibration value, verify Enabled has been selected, and select OK Enter a carousel number in tube one position Select Run 9

DataBase QC Product Editor Editing a Product From the Report Generator toolbar select Product Editor Select the desired product you wish to edit Select the desired information field to be edited Make the change Repeat the process for each field When finished, select Save Prod then select Yes to confirm update to the lot number Entering a New From the Report Generator toolbar select Product Product Editor Select the New Product button Select the first information field Enter the information Repeat the process for each field When finished, select Save Prod then select Yes to confirm update to the lot number Quality Control Report Sample data is sent to the database when samples are run and the protocol region properties are set correctly Setting Region Drag and drop a protocol to the workspace Properties Save the previous protocol or not as desired Select a region for statistics to be sent to the database Right click the mouse and select Region Properties Select Region statistics to be exported for Quality Control Select a QC Product and select OK Repeat for each region to be used Save the protocol Activating QC Select on the Report Generator Template toolbar (one time procedure) Change instrument to Default Select Template >> Select Template Select desired template and then Open Select Template >> Save Template to save the template with the system serial number Repeat process for each template 10

Select a Template Select on the Report Generator toolbar Select Template >> Select Template Select desired template and then Open Select a point Left click on the point (a red line appears) Creating a New First, enter the new QC product (earlier in database) QC Template and ensure the protocol has regions selected for QC export with a QC product Run the protocol at least once Panel Template Select on the Report Generator toolbar Select Template >> Clear Template Select New Plot button Click on the header portion of the plot Select user label and select a label from the list or enter the desired label Select the QC protocol from the list Select the appropriate QC product Select the lot number Select a parameter or region Select X or Y axis Select a statistic When finished, select OK Repeat process for each new plot When finished, select Template >> Save As Enter a name and select Save Accessing a template Select on the Report Generator toolbar Select File >> Open and locate the desired template Select the template and then Open Creating a Template First create a panel and then save the panel with the Export results of panel to report Generator selected Select Panel Template on the Report Generator toolbar Select File >> Open and locate the new blank template Select the template and then Open Select the desired global options on the Local tab 11

Select each field in turn and enter the desired information Select Update to enter the information and clear the fields Or Select Update & Retain to enter the information only Repeat for each line Select Data Plots tab to add plots When finished, select File >> Save Panel Report Select Panel Report on the Report Generator toolbar Select Search button to list reports Highlight desired report and then click on Select Database Entry Select on the Report Generator toolbar Select New Enter information in each desired field and select Save Maintenance Log Select, double click on item to log Service Log Select, select field and enter information 12

Offline Analysis Retrieve with Runtime Select Listmode tab on the Resource Explorer Protocol (protocol used Locate the desired listmode file and drag and drop To collect the data) the file to the Workspace If asked do you wish to clear acquisition data, answer Yes Save previous protocol as desired The protocol appears and the data shortly after Retrieve with a Different Select Protocols tab on the Resource Explorer Protocol Locate the desired protocol drag and drop it the Workspace If asked do you wish to clear acquisition data, answer Yes Save previous protocol as desired Select Listmode tab on the Resource Explorer Locate the desired listmode Drag and drop it to any one of the plots on the Workspace The protocol will populate with the data Retrieve Multiple Listmode Select Tools >> Listmode Playback Files with Runtime Protocols Right click on Add Protocol tool in the window Select New Worklist Select Add Protocol tool once for each addition protocol Under the LMD File column, select Open File icon Select the desired listmode file and then Open Repeat for all listmode files Select the Options tab and other desired options Select the Single File Mode tab Select the Run tool in the window The files are displayed Files with Different Protocols Same as previous action but with one addition: 13

Select the Open Protocol icon under the Protocol column Select the desired protocol and then Open Repeat for each protocol Batch Automator Select Tools >> AutoMATOR Setup To remove old selected files from the list: select the files and then the Remove Files button Select Add Files Select the desired files and then Open To change the order: Select a file and drag and drop it to a new position Select the desired process option next to the files ( pass, pause 12 seconds, stop and wait to restart) Select the desired output option To process: Select Run on the Automator toolbar Listmode Playback Tool Select Tools >> Listmode Playback Select either the Add Protocol or Add Panel Select Open for the first listmode file Select the listmode file and then Open Repeat for each listmode file If desired, select the Open for each protocol in turn Select the desired protocol and then Open Select Options tab and desired options Select Single File Mode tab Select tool in the window The files are displayed Publishing Set Preferences Press CTRL + W and select Publish tab Select the desired publishing option Publish to Text File or Publish Data to MS Excel or both Select desired data format Select desired bitmap size 14

Select desired File References option Select whether or not to switch to Excel on publish Output Select Tools >> Publish Results Now Enter name and select Save System opens MS Excel and displays data Assigning Color to Dot Plots Press CTRL + W and select Gating tab Color Precedence Select Automatic Color Precedence Select Color Precedence Setup on the toolbars Edit colors as desired Move regions using a drag drop technique Color will be assigned to dots based on the color located highest on Precedence list (top position) Color Blend Select Color Blend Mode Select Color Blend Setup Select 3 different regions to blend Color will be assigned based on the number of the regions satisfied by the event Copy and Paste Copy Image Select a plot Right click and select Copy Plot Image Paste Image Open the desired program (e.g. PowerPoint, Word) Select desired area Select Edit >> Paste Copy Data Select plot Right click and select Copy Plot Data Paste Data Open the desired program (e.g. MS Excel) Select desired area Select Edit >> Paste Freeze Single Histogram Run a sample or retrieve a listmode file Plots Choose a histogram plot to apply freeze frame 15

Move the cursor to the lower right corner of the plot Until appears Left click and select the Histogram tab Select Freeze Frame and then OK Run another sample or retrieve another file, an outline of the previous file appears on top of the new file You can repeat the process to achieve 2 freeze frames on top of a new file Baseline Offset Select File >> Workspace Preferences Select Plot Display tab Select Baseline Offset On System adds a randomized positive Gaussian offset to the low channels bringing the negative population out from channel zero on log displays Listmode Compensation Select Listmode tab on the Resource Explorer Select desired listmode file Drag and drop it to the workspace Select Analysis >> LMD Quick COMP Adjust the slider bars to change the compensation The data responds accordingly Save recompensated file (file extension will be CMP) 16

System Setup Administration Functions Select a the user with administration privileges Enter the user password Select Admin button Select the user, enter both the user and administration passwords and select OK Add a User Select Add User Enter user name, first name, last name and title Select desired privileges Select Change and enter a user password Optional: Select Paths tab and change user paths Group Users Select Workgroups Select Edit and then Add Rename your workgroup as desired Select all users to be included in the workgroup Track User Usage Select Export Log Enter range of dates and select Next Select users to be included in the billing file Select Next Select to send to clipboard or file and select Delimiter Select Finish and then Close Unlock a User Select user Select Modify User Select Unlock User Archive Select Archive Data Select Archive location Select dates Select data to archive Select Archive and then OK Select Close 17

Workspace Preferences Select File >> Workspace Preferences File Naming Select LMD Filename tab Select items to be part of the filename Plot Display Select Plot Display tab Select desired options Gating Select Gating tab Select desired options Acquisition Select Acquisition Options tab Select desired output options User Info Publish Select User Info tab Enter desired user information Select Publish tab Select desired publishing format options 18